Studies in Alternative Relationships
by virginiagirl101
Summary: An alternate version of season 2 in which Jeff are in a secret relationship. Will cover at least one scene per episode.
1. Anthropology 101

**AN: So I decided to do my version of a "season 2 with Jeff and Annie in the secret relationship fic". I already have it planned out, I just have to write it—it looks like it will be 24-27 chapters, one for each episode with maybe extras. Please let me know what you think, I hope you enjoy!**

**Disclaimer: I own nothing.**

**Summary: An alternate version of season 2 in which Jeff are in a secret relationship. Will cover at least one scene per episode.**

_Anthropology 101_

The day after he is brutally attacked in Anthropology, Jeff is walking down the hall after his "Patterns and Puzzles 101" class, for which he gets 3 math credits for trying to figure out what number comes next. Although he hasn't seen the group as a whole for the day, he has seen a few of them—Abed and Troy, who were wearing black, holding a mouse, and informed him that 'you didn't see us. Or Fievel. In fact, this never happened, especially if the Biology teacher or Pierce asks'; Britta and Shirley, who were gleefully gossiping as they walked down the halls towards him; and even Pierce, who asked him if he'd seen 'Troy, Abed, and that damned rat', to which he dutifully responded with a 'no'. In fact, the only person he hadn't seen was Annie.

Just as his thoughts turned to her, he sees said study group member walking down the hall that crossed his and lead to the cafeteria. Because he is a) bored, and b) has nothing better to do, he follows her. She is quite a ways ahead of him, so by the time he makes it to the cafeteria, she has disappeared. He stands in the doorway, looking around before spying her sitting down in a corner table by the window. He heads over to her, he gets distracted by a wonderful smell, and notices that the coffee shop has just brewed a fresh pot. Hesitating, he reasons that she will still be there once he buys his coffee, and hey! He can buy her coffee too, as an apology. Plus, he's really tired and didn't sleep well the night before because of his injuries, so really his distraction at the siren call of caffeine is partly her fault.

By the time the disgusting concoction she calls coffee is finished, it is ten minutes later and he has tried to relentlessly avoid the glares of three women while waiting desperately for his coffee to cool. Also, he heard a couple noises/voices from the vents that sounded suspiciously like Troy and Abed, but whatever. He's ignoring it.

He makes his way over to where Annie is sitting. She isn't eating anything, but rather she has pulled out a text book and a notebook for one of her classes and is scribbling away furiously. "Hey Annie," he greets her.

She jumps, startled, before looking up at him. "What do you want?" she asks.

"I'm just curious as to what you're up to."

She glares at him. "I'm studying."

He nods. "I can see that. Is there any reason you're doing it in the cafeteria?"

"Where else would I do it?" she inquires archly.

"Um, the library, where people study. Or, you know, the study room, which has the word "study" in it."

She sighs. "Britta and Shirley are in there."

He raises an eyebrow at her. "So?"

She groans. "So they're probably still mad at me about the kiss thing!"

He sighs, sitting down across from her and pushing her cup towards her. "Annie. I'm pretty sure we resolved this yesterday."

She stared at him. "Just because we're all talking again doesn't mean everything's okay, Jeff. I mean, we kissed right after Britta _declared her love for you_."

"She didn't mean it," he interjects.

She rolls her eyes. "So she says. However, that's not what she was saying at the time. Which means that us kissing could have hurt her awfully. And I didn't even care! I got caught up in my old fantasies of a perfect life and only focused on myself. So I understand why they are mad at me, but that doesn't mean I want to deal with it."

He looks at her. He doesn't want to touch most of that, but the first part . . . "what do you mean 'so she says'?"

She huffs. "Well the two of you were acting pretty lovey dovey yesterday and she didn't seem to be complaining!"

He stares at her in shock. "You do realize that was all so we could be the 'good guy' in the eyes of the public right? It wasn't real, or anything, it was like a staring contest."

"Okay, what about when you slept together?"

He groans. "Annie, it didn't mean anything, okay? None of it meant anything, it was just us being stupid."

She snorts. "Don't be ridiculous, Jeff, you were after her all last year."

He rolls his eyes. "Strangely my attraction to her ended as soon as she publicly declared her love for me!"

She's shocked at that, looking as if she's been slapped. "Is that why you stopped being attracted to me?"

"What?" He asks, unsure of what this is going.

"I mean, I kissed you first, I'm obviously more into you than you are into me. Is my having feelings for you why you stopped being attracted to me?"

He groans, before looking at her. "Annie, no. You and me, it's just a really bad idea. Besides, I'm 'gross', remember?"

She nods, blushing. "Sorry, I shouldn't have brought it up," she says, looking down.

He stares at her for a while, feeling strangely guilty. "Look, Annie," he starts. "I'm sorry I ignored you all summer. I was scared of how you would react to the kiss, so I was trying to be adult enough for both of us, but I overdid it. I'm also sorry for how I acted with Britta—it wasn't about you, it was about me. It's just proof as to how I'm old and gross, and you should be with someone young and nice, okay?"

She doesn't really respond, but she's looking at him. "I'm sorry I punched you, I guess," she tells him.

"You guess?" he asks in mock outrage. "Just for that I'm leaving you to your studying!" he gets up, acting stand offish on purpose. "I hope you enjoy yourself madam!"

She nods, giggling. As he walks away, she calls out "Jeff! See you at study group?"

He turns around and nods, before walking away and feeling like he's finally doing this year right.

**AN: I hope you enjoy! I'm not sure about my characterization of Jeff—I feel like at this point, he's the type of person who makes a mistake, then goes out of his way to fix it before forgetting about it and getting caught in the same loop. Also, I feel like he's nicer to you one on one than he is in a group, except when he's distracted, like with that stupid competition with Britta. As for Annie, I feel like she would want to know 'why' Jeff isn't attracted to her, as she likes data and wants to fix things. But of course he **_**is**_** attracted to her, so he's vague cause he doesn't want her to change.**


	2. Accounting for Lawyers

**An: So onto **_**Accounting for Lawyers**_**! This is one of my favorite season 2 episodes. I love the Annie/Troy/Abed shenanigans, and of course Jeff's pop and lock skills. Please review!**

**Disclaimer: Dan Harmon owns it all.**

**Summary: Post **_**Accounting for Lawyers**_**, Jeff and Annie talk about the party.**

_Accounting for Lawyers_

As the study group sat around after the pop and lockathon, with Troy and Abed recounting the story of their epic caper, Jeff half tunes them out to think back to the events of the past few days. Running into Alan had been very unexpected. He wasn't sure what he was expecting—maybe mocking words and laughter, but instead Alan had been strangely . . . nice about the whole thing. Sure there was some mocking language, and Jeff was fully aware he had been buttering him up for the whole promotion thing, but still, it could have been a lot worse.

Speaking of things that could have been a lot worse—that party could have been a lot worse. Luckily he had managed to reduce the damage by (mostly) keeping track of the study group—although he had failed to notice Troy, Annie, and Abed sneaking off until it was too late (and from what he could hear, poor janitor). However, he does have to admit that he'd rather have Troy and Abed away from the party and on one of their capers than potentially embarrassing him by harassing his former, and hopefully future, coworkers. He had also managed to make sure Britta hadn't maimed/insulted/argued with his coworkers, who were like him, but worse; had talked Shirley out of suing anybody—she probably would have been eaten alive in fees; and had convinced Pierce that hunting men for sport was so morally wrong even he wouldn't have been able to get away with it. He'd even managed to keep Alan from absconding with Annie for too long. And the best part was he totally _rocked_ the pop and lockathon, at least before his own team sabotaged him.

As he comes back to the conversation, the others are saying goodbye for the evening and starting to head back to the parking lot, and their cars. He starts to follow them, before noticing that Annie is hanging back, purposely taking a long time to get her stuff. He stops, looks at something on his phone, and waits for her to catch up.

When she notices him waiting, she looks surprised. "I thought you left," she tells him when she reaches him.

He shrugs. "I noticed you hanging around and figured if I waited for you it would give me a chance to check my messages."

She rolled her eyes, sounding exasperated. "Of course it did. You know I kind of want to steal your phone to see how you would do without it."

He grins. "I'd like to see you try."

She smiles mischievously at him. "Trust me Jeff, you won't see it coming."

"What are you going to do, chloroform me?"

She blushes slightly. "No" she pouts "Abed and Troy took it away from me."

"I can't really blame them," he informs her seriously. "I imagine neither would the janitor."

"It wouldn't have happened if they hadn't got caught!" she exclaims. "Or if THEY'D come up with an escape plan."

He grins at her. "And you were doing so well too."

She looks at him, confused. "What does that mean?"

He shrugs, uncomfortable and cursing himself for bringing it up. "Fitting in at the party. I mean, you looked the part, you were on the arm of better lawyers, you probably actually have experience with that sort of thing . . ."

She smiles at him shyly. "Really?"

He nods. "Yeah. I mean, we're lucky Alan didn't kidnap you."

She groans, throwing her head back slightly. "I'm lucky you mean. Seriously, Jeff, I don't know how you stand him!"

He sighs. "I told you, I don't care."

She rolls her eyes. "Not that! I mean, it sucks that he sold you out, but he's so _gross_."

He looks at her incredulously. "You dated a shoeless, shirtless hippy."

She nods. "Yeah, but at least he was nice. I mean, you can't deny Alan is gross, can you?"

He sighs. "No. No I cannot." He's quiet for a moment. "You really were the best behaved of all of them tonight," he tells her quietly. "And I wasn't worried about your behavior—at least until you started chloroforming people."

She nods, and they fall into silence. Suddenly, she stops. "Crap," she mutters, digging around in her bag. "I forgot my keys at the pop and lockathon."

He stops too. "Do we need to go back and get them?"

She shakes her head, waving her hand. "Nah, I can get them myself."

"Annie. It's late."

She rolls her eyes. "It's not even Midnight!"

"It's not safe."

"Come on Jeff, it's Greendale." When he still hesitates, she rolls her eyes again. "Look, we're five feet from the doorway, and there's light the whole way."

He raises an eyebrow. "Okay, but what about the parking lot?"

"I'm parked in the second row." When he doesn't move she pushes him. "Stop worrying about me, I think we proved I can defend myself today."

"You said they took away the chloroform!" he exclaims.

She smirks. "A girl's gotta have her secrets, Jeff. Now go."

He sighs, giving in. "Fine. But text me when you make it home, ok?"

She nods, smiling. "I promise."

So he leaves her, cursing himself the entire time. Halfway to his car, he turns around to make sure she got inside the building ok. She must be coming out, because she's paused to look at her phone (and she calls him dependent!).

Fifteen minutes after he gets home, she texts him to let him know she's safe. He puts down his scotch, turns off the TV, and goes to bed.

**AN: I hope you liked it! I am a little bit unsure about the characterizations here—I think for this premise to work, Jeff needs to be softer than he was in canon, so I tried to balance it out, and I hope Annie is okay too.**


	3. Psychology of Letting Go

**AN: So . . . I'm back. Sorry about the length in between updates, school really sucks (and I'm procrastinating on a midterm to write this, so you should feel lucky). So I hope you enjoy, and please review. And thanks to Lunarblue21 for the beta!**

**Disclaimer: I own nothing, Dan Harmon does, blah blah blah, the usual.**

**Summary: Jeff has just about reached his car when he hears her voice.**

_Psychology of Letting Go_

Jeff has just about reached his car when he hears her voice.

"Jeff. Jeff, wait up!"

Sighing, he turns around. All he really wants to do is go home, drink some scotch, and crawl into bed while pretending today never happened (especially the parts with his cholesterol and Pierce. The part with Annie and Britta in oil hugging . . . that might be allowed to stay). As he turns around, he is unsurprised to see a familiar brunette in a splattered 'Save the Gulf' T-shirt. "Annie," he says when she reaches him. "What do you want? And make it snappy, please."

Annie shifts on her feet a little. "I just wanted to make sure you're okay."

He nods, smiling at her for the first time. "I'm fine, Annie. I've come to terms with the fact that nobody is perfect, and that includes me, unfortunately. Besides, it could be worse. It could affect my gorgeous body," at her rolled eyes he continues "seriously, Annie, do you _want_ my looks to be messed up? That would be a tragedy."

She nods, grinning. "Of course, I don't know how the world would survive."

He smirks at her. "Well, don't worry, my body and I are fine. Pierce's mom helped out a lot."

She raises her eyebrow. "That sounds like a story," she tells him with a grin.

He nods at her. "It is. I'll tell you more tomorrow, when Britta and Shirley could hear."

At that, her face falls slightly. "Sounds like a plan."

He sighs, knowing he shouldn't ask, but being unable to resist. "Annie. What's wrong?"

"Hm?" she asks, seeming surprised. "Oh, it's nothing."

"Mhmm," he says, giving her the look that gets everyone to crack.

She shifts under her gaze. "Doyoureallynotbelieveyoumadeoutwithme?" she says in one sentence.

He laughs nervously. "Um, you'll have to run that one by me again. I don't speak gibberish, sorry."

She shifts again. "Never mind, it's stupid," and she turns and walks away.

Sighing, he catches her arm. "Annie, seriously. I didn't even understand what you said. Speak slower."

Turning around, she faces the ground, speaking just loud enough for him to hear her. "Before, with Britta, you said . . . do you really not believe you made out with me?"

He lets go of her arm, laughing nervously. "Annie. Come on. The two of you were being totally immature, and fun ruiners. You were ruining my fun."

She glares at him. "Oh, because you were being so mature yourself! AND you were totally ruining Pierce's fun!"

He smirks at her. "Yes, but Pierce and I never made out."

She rolls her eyes and starts to walk away again. "Annie. Come on, I was joking."

She stops, but doesn't turn to look at him. "No, you know what? It was a stupid question. Obviously you were telling the truth, or you wouldn't have been so ashamed of it. At least it's not just me though."

He rolls his eyes. "Annie, I can believe I made out with you. Believe it or not, I remember what I was thinking that night very well. That doesn't mean we should be together, or that we should be making out all the time though."

She turns back to him, looking vulnerable. "Really?"

He nods. "Yeah really. Come on, you're great. Any guy would be dumb to _not_ want to make out with you."

She smiles, blushing. "Thanks, Jeff."

He laughs. "Now, if you'll excuse me, I'm treating myself to pizza with actual cheese. And regular crust. This hasn't happened for over thirteen years."

She smiles softly. "Sounds like a good time."

He nods seriously. "It is. It's a very good time. It's the best time." She rolls her eyes, giggling. "Are you doubting me, Annie Edison?"

She laughs, "I'm sorry, I guess we have different definitions of a good time."

He gives her an affronted look. "Well maybe I'll have to prove my good time expertise to you."

She stops laughing to look at him shyly. "Maybe you will."

His look softens into a smile. "Well that pizza won't eat itself."

She chuckles again, shaking her head. "No it won't." and she starts to walk away.

"Drive safely!" he calls after her.

She holds one thumb over her head without turning around.

Smiling, Jeff climbs into his Lexus and drives away.


End file.
